Bioinformatic analysis of potential candidates for therapy of inflammatory bowel disease
EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES
Authors: Li, X. -L.; Zhou, C. -Y.; Sun, Y.; Su, Z. -Y.; Wang, X.; Jia, E. N.; Zhang, Q.; Jiang, X. -F.; Qi, W. -Q.; Xu, Y.
Abstract
OBJECTIVE: Inflammatory bowel diseases (IBDs) including ulcerative colitis (UC) and Crohn's disease (CD) increased the risk for developing colorectal cancer. However, there is no effective therapy for IBDs. The aim of this study was to identify potential therapeutic targets for inflammatory bowel disease (IBD) and explore the possible mechanism underlying this disease. MATERIALS AND METHODS: Gene expression profile GSE6731 was downloaded from Gene Expression Omnibus database, which included 9 UC samples and 19 CD samples. Differentially expressed genes (DEGs) between affected colon tissues and non-affected tissues were identified in UC and CD group. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis of DEGs were performed. Modules in the protein-protein interaction (PPI) network were identified, and significant node genes were selected. RESULTS: Total 619 DEGs including 285 up-regulated genes and 334 down-regulated genes were identified in UC group and total 1159 DEGs of CD including 585 up-regulated genes and 574 down-regulated genes were selected. Module was selected from PPI network. From the PPI network and module, DEGs of mitogen-activated protein kinase 3 (MAPK3), N-myc downstream regulated 1 (NDRG1) and major histocompatibility complex, class II, DR alpha (HLA-DRA) have high degree. CONCLUSIONS: MAPK3, NDRG1 and HLA-DRA may play key roles in the progression and development of IBD. They may be used as specific therapeutic targets in the treatment of IBD. However, further experiments are still needed to confirm our results.
Introduction of exogenous class II trans-activator in MHC class II-deficient ABI fibroblasts results in incomplete rescue of MHC class II antigen expression
JOURNAL OF IMMUNOLOGY
Authors: Peijnenburg, A; Gobin, SJP; vanEggermond, MCJA; Godthelp, BC; vanGraafeiland, N; vandenElsen, PJ
Abstract
Previously, we have shown that fibroblasts established from type III bare lymphocyte syndrome patient ABI are characterized by the absence of MHC class II gene expression and a strongly reduced amount of MHC class I transcripts. Complementation analysis has suggested that the gene defective in these ABI fibroblasts is different from that encoding the class II trans-activator (CIITA), which has been attributed an essential role in both constitutive and inducible expression of MHC class II genes. In the present study it is shown by reverse transcriptase-PCR analysis that the amount of CIITA transcripts in ABI fibroblasts is greatly reduced compared with that in fibroblasts derived from a healthy individual, Transient cotransfection of a construct in which CIITA is under the control of a constitutive promoter with an HLA-DRA promoter-luciferase reporter plasmid resulted in enhanced luciferase expression in ABI fibroblasts. Furthermore, ABI fibroblasts stably transfected with CIITA re-express functional HLA-DR Ags, but do not express HLA-DQ and DP Ags at the cell surface. Comparison of these data with those obtained for normal fibroblasts and fibroblasts defective for CIITA indicate that the gene defect and the resulting lack of MHC class II expression in ABI fibroblasts can only partly be corrected by the introduction of CIITA. Furthermore, DNase I hypersensitivity analysis of ABI fibroblasts has revealed a closed chromatin structure in the promoter region of the MHC class II DRA gene. However, CIITA transfection resulted in an open DNA configuration, which suggests a role for CIITA in provoking changes in the chromatin structure of the DRA gene.